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Springer Handbook of Bio-/Neuroinformatics pp 151–169Cite as

Bioinformatic Methods to Discover Cis-regulatory Elements in mRNAs

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Part of the book series: Springer Handbooks ((SHB))

Abstract

Cis-regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). Due to these elements, mRNAs may be translated with remarkable efficiency, or destroyed with little translation. Untranslated regions cover over a third of a typical human mRNA and often contain a range of regulatory elements. Some elements along with their RNA or protein binding partners are well characterized, though many are not. These require different types of bioinformatic methods for identification and discovery. The most successful techniques combine a range of information and search strategies. Useful information may include conservation across species, prior biological knowledge, known false positives, or noisy high-throughput experimental data. This chapter focuses on current successful methods designed to discover elements with high sensitivity but low false-positive rates.

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Abbreviations

3-D:

three-dimensional

BLAST:

basic local alignment search tool

CDS:

coding sequence

CM:

covariance model

ChIP:

chromatin immunoprecipitation

DNA:

deoxyribonucleic acid

EST:

expressed sequence tag

FIRE:

finding informative regulatory element

GEO:

gene expression omnibus

HMM:

hidden Markov model

IRE:

iron responsive element

IUPAC:

International Union of Pure and Applied Chemistry

KH:

K homology

MAF:

multiple alignment format

MEME:

multiple expectation maximization for motif elicitation

MEMERIS:

multiple EM for motif elucidation in RNAs including secondary structures

MFE:

minimum free energy

NCBI:

National Center for Biotechnology Information

PDB:

protein data bank

PWM:

position weight matrix

RBPDb:

RNA-Binding Protein DataBase

RIP-chip:

RNA immunoprecipitation chip

RNA:

ribonucleic acid

RRM:

RNA recognition motif

SCFG:

stochastic context-free grammar

SCI:

structure conservation index

SECIS:

selenocysteine insertion sequence

SELEX:

systematic evolution of ligands by exponential enrichment

TFBS:

transcription factor binding site

UCSC:

University of California Santa Cruz

UTR:

untranslated regions

dsRNA:

double-strand RNA

log:

logistic regression

mRNA:

messenger RNA

miRNA:

microRNA

mirSVR:

micro support vector regression

ncRNA:

noncoding RNA

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Authors and Affiliations

  1. Department of Biochemistry, University of Otago, Cumberland Street, 1019, Dunedin, New Zealand

    Stewart G. Stevens

  2. Department of Biochemistry, University of Otago, 710 Cumberland St., 9016, Dunedin, New Zealand

    Chris M. Brown

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  1. Stewart G. Stevens
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  2. Chris M. Brown
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  1. KEDRI – Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, 120 Mayoral Drive, 1010, Auckland, New Zealand

    Nikola Kasabov

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Stevens, S.G., Brown, C.M. (2014). Bioinformatic Methods to Discover Cis-regulatory Elements in mRNAs. In: Kasabov, N. (eds) Springer Handbook of Bio-/Neuroinformatics. Springer Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30574-0_10

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